update system set status=0 where name='alfresco_browser' and type='module';

The CTools CSS cache directory, ctools/css could not be created due to a misconfigured files directory.

This refers to the CSS cache directory in sites/default/files/ctools(not sites/all/modules/ctools), and will also occur if the directory exists and a hidden file (such as .svn) already exists within it.

Also make sure that it is group writable and directory executable:

chmod -R a+X sites/default/files
chmod -R g+rwX sites/default/files

The destination directory is not configured correctly

The Drupal notice File temporary://xxx could not be copied, because the destination directory public://avatars is not configured correctly. means that the folder sites/default/files/avatars (based on your location for public://) does not exist or cannot be written by Drupal.

Fatal error: Class 'CMISService' not found

If you are using the CMIS 2.x module, make sure that you have placed the CMIS library into sites/all/libraries/cmis-phplib/cmis-lib.php, and refresh your cache.